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Media

Software

natverse - a toolscape for neuroinformatics, co-author

neuromorphr - author

neuronbridger - author

hemibrainr - author

mouselightr - author

insectbrainr - author

Main

Alexander Shakeel Bates

I am a neuroscientist and programmer on open-source projects. I work on insect brains. I am interested in how neurons wire together, and how they work together to build complex, innate behaviours. Alive since 23/09/1993.

total_cites h_index i10_index
575 12 12

Professional Research

Visiting Scientist

Dept. Zoology, University of Cambridge

remote

present - 01/10/2020

Postdoctoral Fellow in Neurobiology

Harvard Medical School

Boston, US

present - 01/10/2020

  • Member of the laboratory of Prof. Rachel Wilson
  • Working on navigationaly circuitry, using calcium imaging, neurophysiology and behavioural studies involving virtual reality with D. melanogaster

Grants

EMBO fellow

European Molecular Biology Organization

European

present - 01/04/2021

Life Science Research Foundation Fellowship

Life Science Research Foundation

US

2021

  • Postdoctoral fellowship, gratefully declined

Human Frontiers Fellowship

International Human Frontier Science Program

International

2021

  • Postdoctoral fellowship, gratefully declined

Herchel Smith Scholarship

Herchel Smith Foundation

Cambridge, UK

30/09/2019 - 01/08/2015

Education

Neuroscience PhD

University of Cambridge

Cambridge, UK

30/09/2020 - 01/09/2015

  • PhD student with Dr. Greg Jefferis
  • Thesis: The lateral horn, a brain region in the fly, primes innate olfactory behaviours by combining patterns of second-order olfactory projection neuron activity. In my work, I developed tools and analyses, and reconstructed neural networks from electron microscopy data, in order to better understand this brain region and how memory systems interact with it
  • Neuroinformatics, data science, R programming

Neuroscience BSc

University College London

London, UK

01/07/2015 - 01/09/2012

  • 1st class degree with honours
  • Modules taken listed on linkedIn

A levels

Woodbridge High School

London, UK

01/09/2012 - 01/09/2010

  • 6 As at A-level, comprising: Physics, Chemistry, Mathematics, English Literature, Philosophy and Russian, and A in a history related EPQ (level 3) project

GCSEs

Woodbridge High School

London, UK

31/09/2010 - 01/09/2008

  • 13 A*s: English Literature, English Language, Mathematics, Statistics, Core Science, Additional Science, History, Philosophy, Geography, French, Italian, Russian and Expressive Arts. Jack Petchey Achievement Award

SKILLS

  • R

  • python

  • matlab

  • Git

  • GitHub

  • Markdown

  • Illustrator

  • InDesign

  • text editing

  • communication

  • journalistic writing

  • creative writing

Awards

BNA Postgraduate Prize

British Neuroscience Association

UK

2020

Max Perutz Prize

MRC LMB, University of Cambridge

Cambridge, UK

2020

Boehringer Ingelheim Scholarship

Boehringer Ingelheim Foundation

European

01/08/2018 - 01/08/2016

Rob Clarke Award

Society of Physiology

London, UK

2015

Honorary Vice Chancellor’s Award

University of Cambridge

Cambridge, UK

2015

Burnstock Prize

University College London

London, UK

2015

  • Highest grade in Neuroscience BSc course, 3rd year

Burnstock Prize

University College London

London, UK

2014

  • Highest grade in Neuroscience BSc course, 2nd year

Dean’s list

University College London

London, UK

2014

  • Dean’s list for the Faculty of Life Sciences, awarded based on undergraduate grades

Burnstock Prize

University College London

London, UK

2013

  • Highest grade in Neuroscience BSc course, 1st year

Dean’s list

University College London

London, UK

2013

  • Dean’s list for the Faculty of Life Sciences, awarded based on undergraduate grades

REFEREES

  • PhD Supervisor: Dr. Gregory Jefferis, MRC Laboratory of Molecular Biology, Cambridge, jefferis@mrc-lmb.cam.ac.uk

  • Current Supervisor: Prof. Rachel Wilson, Harvard Medical School, Rachel_Wilson@hms.harvard.edu

  • BSc Tutor at UCL: Dr. Marco Beato, UCL Neuroscience, Physiology and Pharmacology, m.beato@ucl.ac.uk

  • Supervisee: Serene Dhawan, The Francis Crick Institute, serenedhawan@gmail.com

Leadership

President of BlueSci

University College London

London, UK

01/10/2019 - 01/01/2016

  • Lead BlueSci, the University of Cambridge’s science media society, throguh 15 issues of the magazine

Mentored summer student

MRC LMB, University of Cambridge

Cambridge, UK

2018

Mentored undergraduate student

Dept. Zoology, University of Cambridge

Cambridge, UK

01/05/2018 - 01/09/2017

  • Student won best thesis in year award and two authorships

Mentored summer student

MRC LMB, University of Cambridge

Cambridge, UK

2017

LMB graduate symposium lead organiser

MRC LMB, University of Cambridge

Cambridge, UK

2017

LMB graduate symposium organiser

MRC LMB, University of Cambridge

Cambridge, UK

2016

President of the UCLU Writer’s Society

University College London

London, UK

01/10/2015 - 01/10/2014

Science Editor, Pi Magazine

University College London

London, UK

01/10/2015 - 01/10/2014

UCL iGEM Advisor

University College London

London, UK

2014

  • Project planning, oversight, team slection and management
  • Gold medallist

Publications

This table shows all of my work, searchable on pudmed. Get in contact for information on recents projects

title author journal cites year position IF
1 Information flow, cell types and stereotypy in a full olfactory connectome P Schlegel, AS Bates, T Stürner, SR Jagannathan, N Drummond, J Hsu, … Elife 2 2021 1 7.616
3 The connectome of the adult Drosophila mushroom body provides insights into function F Li, JW Lindsey, EC Marin, N Otto, M Dreher, G Dempsey, I Stark, … Elife 36 2020 6 7.616
4 BAcTrace, a tool for retrograde tracing of neuronal circuits in Drosophila S Cachero, M Gkantia, AS Bates, S Frechter, L Blackie, A McCarthy, … Nature methods 5 2020 3 26.919
5 A connectome and analysis of the adult Drosophila central brain LK Scheffer, CS Xu, M Januszewski, Z Lu, S Takemura, KJ Hayworth, … Elife 96 2020 6 7.616
6 Connectomics analysis reveals first-, second-, and third-order thermosensory and hygrosensory neurons in the adult Drosophila brain EC Marin, L Büld, M Theiss, T Sarkissian, RJV Roberts, R Turnbull, … Current Biology 32 2020 6 9.251
7 Input connectivity reveals additional heterogeneity of dopaminergic reinforcement in Drosophila N Otto, MW Pleijzier, IC Morgan, AJ Edmondson-Stait, KJ Heinz, I Stark, … Current Biology 17 2020 6 9.251
8 Complete connectomic reconstruction of olfactory projection neurons in the fly brain AS Bates, P Schlegel, RJV Roberts, N Drummond, IFM Tamimi, … Current Biology 46 2020 1 9.251
9 The natverse, a versatile toolbox for combining and analysing neuroanatomical data AS Bates, JD Manton, SR Jagannathan, M Costa, P Schlegel, T Rohlfing, … Elife 56 2020 1 7.616
11 Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila N Eckstein, AS Bates, M Du, V Hartenstein, GSXE Jefferis, J Funke bioRxiv 6 2020 2 0.000
12 Neural circuit basis of aversive odour processing in Drosophila from sensory input to descending output. P Huoviala, MJ Dolan, F Love, P Myers, S Frechter, S Namiki, … bioRxiv 24 2020 6 0.000
13 Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics AS Bates, J Janssens, GS Jefferis, S Aerts Current opinion in neurobiology 28 2019 1 6.541
14 Functional and anatomical specificity in a higher olfactory centre S Frechter, AS Bates, S Tootoonian, MJ Dolan, J Manton, AR Jamasb, … Elife 54 2019 2 7.616
15 Neurogenetic dissection of the Drosophila lateral horn reveals major outputs, diverse behavioural functions, and interactions with the mushroom body MJ Dolan, S Frechter, AS Bates, C Dan, P Huoviala, RJ Roberts, … Elife 62 2019 3 7.616
16 Neurogenetic dissection of the lateral horn reveals major outputs, diverse behavioural functions, and interactions with the mushroom body. Elife 8 MJ Dolan, S Frechter, AS Bates, C Dan, P Huoviala, RJ Roberts, … Elife 3 2019 3 7.616
18 Automated reconstruction of a serial-section EM Drosophila brain with flood-filling networks and local realignment PH Li, LF Lindsey, M Januszewski, Z Zheng, AS Bates, I Taisz, M Tyka, … bioRxiv 44 2019 5 0.000
19 Communication from learned to innate olfactory processing centers is required for memory retrieval in Drosophila MJ Dolan, G Belliart-Guérin, AS Bates, S Frechter, A Lampin-Saint-Amaux, … Neuron 56 2018 3 14.318

Selected Talks

ECRO meeting

European Chemoreception Research Organization

Trieste, Italy

2019

Boehringer Ingelheim Meeting

Boehringer Ingelheim Fonds

Hirschegg, Austria

2018

MPI Connectomics meeting

Max Planck Institute

Berlin, Germany

2017

ECRO meeting

European Chemoreception Research Organization

Cambridge, UK

2017

Boehringer Ingelheim Meeting

Boehringer Ingelheim Fonds

Hirschegg, Austria

2017

Brains and Roses

Schaeffer and Datta group organised

Montserrat, Catalonia

2016

Selected Posters

UK Neural Computation

University of Nottingham

Nottingham, UK

2019

Boehringer Ingelheim Fonds communication workshop

Boehringer Ingelheim Foundation

Mainz, Germany

2017

Maggot Meeting

Janelia Research Campus

Ashburn, US

2016

High-resolution circuit reconstruction meeting

Janelia Research Campus

Ashburn, US

2016

LMB GSA Symposium

MRC LMB, University of Cambridge

Cambridge, UK

2016

Other

Visiting Scholar

Janelia Research Campus

Ashburn, US

2019

Paris Spring School in Neuroscience Techniques

Cambridge, UK

Cambridge, UK

2018

  • A course in Optical Imaging and Electrophysiological Recording in Neuroscience

Visiting Scholar

Janelia Research Campus

Ashburn, US

2016

University of Queensland Winter Scholarship

University of Queensland

Brisbane, Australia

2015

Amgen Scholarship

Dept. Zoology, University of Cambridge

Cambridge, UK

2014

UCL iGEM

University College London

London, UK

2013

  • Team member, cloning, cell culture, project planning
  • Gold medallist

Summer student in the biomolecular modelling laboratory

Cancer Research UK, London Research Institute

London, UK

2013

  • Student Placement with Dr. Tammy Cheng, python programming

Disclaimer

Made with the R package pagedown and datadrivencv.

Code available on GitHub.

Last updated on 2021-07-18.